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The International Consortium of the Chromosome-Centric Human Proteome Project

9th C-HPP Workshop in Busan (Haeundae Ocean Beach), Korea


Final Version: Feb 4, 2014

AGENDA

08:00-09:30 Session 1: Discussion on the Revised C-HPP Long-term Plan

Title: Greetings & Introduction

  • Update on the C-HPP Progress (1st year: Sept 10, 2012-Sept 9, 2013)
  • Revised Goals and Deliverables of the C-HPP (Revised 10 Year Plans),

Extensive discussion will be focused on the formation, rescheduling and targeted deliverables for the newly established phase 1, 2 and 3 of the C-HPP long-term plans. Moderated by Young-Ki Paik, Chair, YPRC, Seoul, Korea, Bill Hancock, Co-chair, Northeastern Univ., Boston, USA (call-in), György Marko-Varga, Co-chair, Lund Univ. Sweden.
The Agenda and Introduction by Yopung-Ki Paik is available in here.
The presentation of György Marko-Varga on Biobanks is available here.
The slides on Wiki update presented by Peter Horvatovich is available here (in ppt) and here (in pdf).

09:30-10:10 Session 2: Discussion on the MRM Standardization for the C-HPP

Title: Large-scale Inter-lab MRM Initiative for the C-HPP and Plans for the Big paper publication plans

  • Overview of the standardization kit developments and its application to quantitative plasma proteomic studies
  • Strategy and update of the large-scale, inter-lab MRM study toward global standardization.
  • Outline of publication plans for the large-scale study and discussion on future standardization initiatives.

Presented by Christoph Borchers Chr 6 group, Genome British Columbia Proteomics Centre, University of Victoria, St. Victoria, Canada. Presentation is available here.

10:10-10:50 Session 3: Plenary Lecture 1- MRM & Glycoprotein Analysis

Title: MRM-based analysis of protein isoforms and automatic analysis of site-specific N-linked glycoproteins
This lecture covers two key topics: an MRM-based quantitative analysis of protein isoforms and GPA, a patented platform for automatic analysis of glycoproteins. Presented by Jong Shin Yoo Chr 11 group, Korea Basic Science Institute, Ochang, Korea. Presenation is available here.

10:50-11:10 Coffee Break

11:10-12:00 Session 4: Discussion on the C-HPP Milestone Papers

Title: Next Big Paper: Contribution of each chromosome team to the major milestones in discovering missing proteins and parts list per chromosome

  • C-HPP Co-chairs will present the overall strategy, timeline and contents for this landmark paper that targets the middle of 2015.
  • Supportive Roles for neXtProt, GPMDB, PeptideAtals and HPA to catalogue the missing proteins in coordination with each chromosome team
  • A strategy for the actual cross-links with B/D-HPP teams

Moderated by Young-Ki Paik, Chair.
Presenation of Jason Neo entitled "AB SCIEX SWATH™: Applications in Biology" is available here.
Presenation of Pengyuan Yang entitled "CN-HPP and CN-C-HPP" is available here.
Presenation of Juan Pablo Albar on Spanish Chromsome Consortium, chromosome 16 is available here.

12:00-13:30 Lunche (Conference Room)

Principal Investigator Council Meeting (TBA)* (Call-in participation)

13:30-14:10 Session 5: Plenary Lecture 2 – Genomics and Transcriptomics

Title: Discovery of Druggable Targets from Liver Cancer Genome**
Presented by Hyun Goo Woo, Dept. of Physiology, Ajou University School of Medicine, Suwon, Korea. Presenation is available here.

  • This lecture covers chromosome-based liver cancer genes and gene clusters which will be a good basis for our joint (C-HPP and B/D-HPP) efforts on the disease biomarker discovery.

14:10-14:50 Session 5: Plenary Lecture 3 – Use of ENCODE Data

Title: Introduction of ENCODE data for potential linkage with Proteomics Research***
Presented by Sung-Min Ahn, Department of Oncology, Department of Biomedical Informatics, Asan Medical Center, University of Ulsan College of Medicine. Presenation entitled "Introduction of ENCODE" is available here.

  • This talk will focus on the use of ENCODE in the proteomics research which fits well to our working scheme. He has been working on both genomics and proteomics and will give us a vision as to how we can merge two disciplines into the C-HPP.

14:50-15:30 Session 6: Transcriptomics & ENCODE: Invited Short Talks and Discussion

Title: Production and presentation of new integrated omics data including transcriptomic RNA Seq and ENCODE data sets in the C-HPP works

  • Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines. Presented by Carol Nilsson (C-HPP EC member and Chr 19 Group), UTMB, Galveston,Texas, USA. Presentation is available here.
  • Transcriptomic maps for all chromosomes using RNA-Seq data from ENCODE, Presented by Alberto Pascual-Montano (C-HPP Chr 16 Group), Centro Nacional de Biotecnología - CSIC, UAM Campus Cantoblanco, Madrid, Spain Spain. Presenation is available here.

15:30-15:50 Coffee Break

15:50-17:30 Session 7: C-HPP Bioinformatics Forum: Invited Short Talks and Discussion

Title: Update on the neXtProt
Presented by Lydia Lane, SIB, Switzerland. Presenation is available here.

Title: Update on the Major Genome-wide ProteomeDBs, Chromosome 1, 8, 20: CAPER 2.0.
Presented by Ping Xu, BPRC, Beijing, China. Presenation is available here.

Session 8: : Progress Reports from Individual Chromosome Teams/Discussion

Part A: Chr 8 and 14
Chairs: Ravi Sirdeshmukh, CSIR, Hyderabad, India and Andrea Urbani, Univ. of Rome, Italy.

  • Chromosome 8: Looking for missing protein further with cell function. Presented by Pengyuan Yang, Fudan Univ., Shanghai, China. Presenation is available here].
  • Bioinformatics pipelines and methodology for the discovery of missing proteins. Presented by Jerome Garin, CEA, France. Presenation is available here.


Part B: Chromosomes 18 and 20
Chairs: Visith Thongboonkerd, Mahidol University, Bangkok, Thailand and Jerome Garin, CEA, France.

  • Chromosome 18 TranscriptoProteome: update 2013. Presented by Andrey Lisitsa, Russian Academy of Medical Science, Moscow, Russia. Presenation is available here.
  • Translating evidence and chromosome-centric human proteome investigations. Presented by Qingyu He, Jinan University, Guangzhou, China. Presenation is available here.


Part C: Mitochondria and KC-HPP Group Activities (Chr 9, 11, 13)
Chairs: Toshihide Nishimura, Tokyo Medical Univ., Tokyo, Japan and Daniel Figeys, Ottawa Univ., Ottawa, Canada.

  • Progress on the Studies of the Subunit 4 of Complex (MT-ND4L). Presented by Andrea Urbani, Univ. of Rome, Italy. Presenation is available here.

17:30-17:55 Session 8: Future Plans on the C-HPP Workshops in 2014/2015

Chairs: Young-Ki Paik and György Marko-Varga

  • 10th C-HPP Workshop: Bioinformatics Janboree in Bangkok, Thailand (August 9 after AOHUPO Congress) by Visith Thongboonkerd, Bangkok, Thailand. Presenation available here.
  • 11th C-HPP Workshop during the Madrid Congress, Spain, Oct 5-8, 2014. Juan Pablo Alba, Centro Nacional de Biotecnología - CSIC, UAM Campus Cantoblanco, Madrid, Spain. Presenation available here.
  • 12th C-HPP Workshop during the Milan EXPO in conjunction with the EuPA Congress 2015, June 23-28th 2015, Milan, Italy: Presented by Paola Roncada (Università degli Studi di Milano). Presenation available here.
  • Updated info obtained from HPP EC conf. calls (Jan/Feb/March) and C-HPP Bioinformatics calls (Jan 26) will be given to all participants.

17:55-18:00 Conclusions and Closing
  • Summary on the Action Plans

The end of C-HPP Workshop

18:30-20:30 C-HPP Dinner


Note:
*Only PIs or their designated representatives can attend this meeting (25 Chr teams)

** References
1. Kwon SM et al., Woo HG. Genomic copy number alterations with transcriptional deregulation at 6p identify an aggressive HCC phenotype. Carcinogenesis 2013 Jul;34(7):1543-50.
2. Woo HG, et al., Exploring genomic profiles of hepatocellular carcinoma. Mol Carcinog. 2011 Apr;50(4):235-43.
3. Woo HG et al., Association of TP53 mutations with stem cell-like gene expression and survival of patients with hepatocellular carcinoma. Gastroenterology. 2011 Mar;140(3):1063-70.

***References
1. Ahn SM et al., The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res. 2009 Sep;19(9):1622-9.
2. Kim D et al., and Ahn SM. Revising a personal genome by comparing and combining data from two different sequencing platforms. PLoS One. 2013 Apr 8;8(4):e60585.
3. Ahn SM, Simpson R, Lee B. Genomics and proteomics in stem cell research: the road ahead. Anat Cell Biol. 2010 Mar;43(1):1-14.

Acknowledgement
This workshop is supported in part by a grant from the Korean Ministry of Health and Welfare (to YKP, HI13C2098).